scPDB - 3dfr entry

Protein Data Bank Entry:

PDB ID : 3dfr

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 1982-06-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydrofolate reductase
ID:	DYR_LACCA
AC:	P00381
Organism:	Lactobacillus casei
Reign:	Bacteria
TaxID:	1582
EC Number:	1.5.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	17.004
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.389	536.625

% Hydrophobic	% Polar
66.67	33.33
According to VolSite

Ligand :

HET Code:	MTX
Formula:	C20H20N8O5
Molecular weight:	452.423 g/mol
DrugBank ID:	DB00563
Buried Surface Area:	62.81 %
Polar Surface area:	216.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-2.65748	34.8994	22.712

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
NA4	O	LEU- 4	2.69	150.97	H-Bond (Ligand Donor)	false
C9	CD2	LEU- 19	4.41	0	Hydrophobic	false
CM	CG	LEU- 19	3.87	0	Hydrophobic	false
N1	OD1	ASP- 26	2.63	169.96	H-Bond (Ligand Donor)	false
NA2	OD2	ASP- 26	2.88	176.45	H-Bond (Ligand Donor)	false
CG	CB	LEU- 27	4.41	0	Hydrophobic	false
C12	CD2	LEU- 27	4.12	0	Hydrophobic	false
CB	CB	ARG- 31	4.11	0	Hydrophobic	false
C9	CG2	THR- 45	4.27	0	Hydrophobic	false
C9	CE1	PHE- 49	4.09	0	Hydrophobic	false
C12	CG	PRO- 50	4.37	0	Hydrophobic	false
C16	CD1	LEU- 54	4	0	Hydrophobic	false
O1	NH1	ARG- 57	2.68	161.79	H-Bond (Protein Donor)	false
O2	NH2	ARG- 57	3.04	168.7	H-Bond (Protein Donor)	false
O1	CZ	ARG- 57	3.7	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 57	3.87	0	Ionic (Protein Cationic)	false
NA4	O	ALA- 97	2.89	127.05	H-Bond (Ligand Donor)	false
C9	C5N	NDP- 163	4.34	0	Hydrophobic	false